Can you repair scratches on filters.

No. You'll ruin it. If it's only one scratch, even a deep one, it probably won't make any difference anyway. But if there are lots of scratches, maybe from too much enthusiastic cleaning, then they will cause flare. In which case bin it; they're cheap.

If you're worried about it, position the scratch over the centre of the lens and shoot a plain surface at minimum aperture (highest f/number) and closest focusing distance. If nothing shows up, then don't worry.
 
I would say it depends on the filter and the scratch, if it's a deep scratch probably no chance, if it's minor some very mild glass polishing compound might get it out. That said you may damage the filter, and if it's minor theres probably no point in bothering.As already said you'd be supprised what marks you can get away with.
I once shot with a very badly cracked skylight filter (couldn't get it off in the field) at f4 on a 50mm you couldn't really see anything much on the prints, even looking. Wayne
 
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